Category: Microbiology

Posts that are Microbiological in nature

More Search Amusements. (p.s. I Ain’t Dead Yet.)

A bit longer of a delay between posts than I’d like, but here you go:

+ =?????

I am often amused (and regularly baffled) by the kinds of search queries that lead people to this blog.

I wrote a sloppy little script to parse the server’s access logs and figure out who’s searching for what, where. Since I added the ability to recognize Google Image Searches, it’s gotten even stranger.

I do get a lot of perfectly understandable hits – people looking for information about “heat-fixing slides”, expired jello, and looking for pictures of lactic-acid bacteria or whatnot. Some of them are pretty interesting questions…but first, some oddities.

At the top of my current wierd-o-meter: “carbonated leprechaun”…what??? What’s funnier is that this was a Google Image search – someone doesn’t just want information ABOUT carbonation of leprechauns, they want pictures. Now I can’t stop imagining a mash-up of “Darkman” and Leprechaun. Thanks a lot, whoever you are…”I needs me gold! ARGH! SUNLIGHT! [bubblebubblebubble…]”

Another recent one was just a search for the phrase “new england sucks”. As another Image search. Somebody not only doesn’t like New England, but they want pictures of “new england sucks”?…

Less risible but still kind of funny are searches influenced by unfamiliarity with the English language. I have no idea what the search for pictures related to “useful of DNA” was hoping to find. (Uses of DNA? How to “use” [work with] DNA? Diagrams of genetic processes?). I also see a number of searches just based on the name of the blog – people looking for information about furnishing “big rooms”. I have no idea what the search for “name of thing in room” was expected to turn up. This one’s another language issue, but even taking that into account I’m still baffled about this one. I wouldn’t expect google.de to return any useful information for “Sache im Zimmer” (the original search was actually from a Spanish-speaking area, but No Entiendo Espanol, so I’ll use a German analogy instead.)

Or from Sweden: “Aerobic Oxygen fraud”. Somebody’s figured out that we don’t actually need to breathe and that it’s all a ploy by the Oxygen Lobby to enslave us, I guess.

Maybe just because “chemicals” get mentioned here from time to time, I get the occasional hit from someone looking for illegal drug information (either technical or just news of drug busts or whatever). Note to “HILLBILLY METH” searcher: Hillbillies do moonshine. Meth comes from Rednecks. Jeez, doesn’t everyone have to do a semester of Rural Population Stereotype Taxonomy in college anymore?

There are some more relevant and interesting questions that show up here, too.

Oreo CookieI guess someone in southern California used an interesting analogy in their microbiology class, because I recently got a couple of searches from there looking for why the cell membrane is not like an Oreo® cookie. The answer: There’s no “creme” filling. No seriously – the membrane is two layers of the same kind of molecule stuck together. The phrase you’re looking for is “Phospholipid bilayer”. In a way, the molecules are a lot like detergents – they’ve got one end that “likes” water, and a long tail at the other end that doesn’t (much as oil doesn’t). Since the cell is surrounded by and full of water, you end up with one layer with all its hydrophilic ends touching the water outside the cell, and the other layer with its hydrophilic ends on the inside of the membrane touching the water inside the cell, and the hydrophobic ends of both layers all tangled up together in the middle – without anything between them. See? Not like an oreo cookie at all. Aside from this, cell membranes are also squishier and not chocolate flavored most of the time.

I’ll deal with “does beer and ice cream make gas” in another post later…

Give a man a fish, and you feed him for a day…

…but teach a man to fish, and he’ll sit in a boat and drink beer all day.

-== We interrupt this blog post to bring you this important announcement: Happy Birthday, Dad!==-

(His birthday was actually yesterday, but this week of school has been grinding me pretty hard and I’d forgotten all about it. He must be so proud – his son can handle a couple of semesters of biochemistry, complex microbial science, working with dangerous chemicals in a lab…but doesn’t seem to know how to use a simple calendar…I am filled with shame.)

We now return you to your regularly scheduled blog post:

This here critter is our resident fish. “He” is a classic specimen of real, old-fashioned, Honest-to-Aquaman Carassius auratus auratus – the Goldfish. And not one of those poor mutant freaks who can barely swim, either. No this here fish was rescued from the overcrowded “feeder goldfish” tank of a local Wal-Mart®. Handsome, ain’t he? I had a tough time getting even this good of a picture – every time I get near the tank he swims back and forth in front of me frantically, perhaps worshipping me as the magical fishfood god. He’s been here for about three years now, so I think he’s having a much longer life than most of them.

I’ve had no time to get into it, but part of the reason for having a fish is that I have a casual interest in aquaculture. That is, while I don’t currently have any intention of becoming a professional full-scale fish-farmer, the subject is interesting and, I think, very important in the near future. Once we figure out where we’re going to end up living next year and get settled in somewhere, I have considered trying to do the aquaculture equivalent of a backyard garden, though.

I think aquaculture is going to become extremely important in the relatively near future, as we run into the combination of overfishing of natural stocks, water shortages, contamination of natural waters with pollutants that build up in naturally-existing populations of fish, and the overall effects of climate change. I think understanding how to raise healthy and nutritious aquatic food without wasting water or causing environmental problems is going to be a useful set of knowledge to have. (There, see, not only do I love kittens and puppies and want to make the world a better place, but I’m also interested in Sustainable Environmental Practices™. While feeding the hungry. [Uphill. In the snow. With no shoes…]).

You may be wondering what interest an ex-professional-computer-nerd microbiologist would have in tending a pond full of eukaryotes. Well, aside from the obvious “Hey, I can have more than one interest, you know”, there actually is a lot of microbiological activity involved in the natural processes of the fishes’ homes. Plus, of course, the aforementioned beer doesn’t ferment and bottle itself, you know.

Since one of my interests in this context is water conservation, my main interest is in figuring out how to maintain a healthy “closed” system. In an aquaculture context, a “closed” system is one that you don’t normally add substantial amounts of water to. (An example of an “open” system might include raising fish in pens floating in a natural lake, or having a constant stream of fresh ground or river water pumping through your tanks). This poses certain problems, since you have to feed the fish, and this adds an ever-increasing load of potentially uneaten fishfood and especially of eaten fishfood – that is, fish wastes.

Fishfood being digested by either fish or bacteria ends up adding ammonia to the water, which is poisonous to the fish (and crawdads and whatever else is in there). Also excreted is carbon dioxide, which makes the water more acidic, and unused food also dumps sulfur and phosphorous into the system.

If you’ve ever had a fishtank, you may know about the ammonia. Certain kinds of Oxygen-using bacteria can actually get some of their biochemical energy from turning reduced nitrogen into oxidized nitrogen, ultimately turning the ammonia (NH3) into much less poisonous nitrate (NO3). These bacteria tend to colonize the tank’s filter, where they do their thing using the oxygen in the water that flows through. Even nitrate is dangerous if it builds up too much, though. In an aquarium, they usually recommend just taking out some of the tank’s water and replacing it with fresh water every week or two to get rid of the build-up. I’d show you pictures of the bacteria, but I still can’t afford a decent microscope. (sniffle.)

Anyway, I want to build a denitrification column one of these days. There are bacteria that can “breathe” nitrate in place of oxygen, and in the process they can reduce the nitrate back down to plain old harmless nitrogen gas, which just bubbles out of the water. If you build a long, tall tube full of something like gravel that bacteria can grow on, and then pump the water through it slowly, oxygen-breathing bacteria near the bottom of the tube rapidly use up the oxygen in the water, leaving the nitrate. With no oxygen further up the tube, bacteria that can breathe the nitrate instead can grow like crazy, and exhale the extra nitrogen out of the system.

That’s one way of avoiding the need to use up as much fresh water as you’d need if you relied only on replacing the water to get rid of the nitrate.

I’ll save the sulfur and phosphorous parts for another day. Meanwhile, I think the next podcast or two will deal with MRSA, since it’s been in the news so much lately. I normally find the neglected non-medical microbiology more interesting, but the biochemistry and genetics involved with Methicillin Resistant Staphylococcus Aureus (not to mention S. aureus itself) is pretty interesting, and I find the media discussions of it unsatisfying.

Stay tuned…

#1 on Google!

Over on scienceblogs.com’s The World’s Fair, the author has started an amusing meme.

It goes like this: the challenge is to find 5 sets of search terms for which your own blog or site is the #1 hit on a Google search. Note that it is acceptable to quote specific phrases but of course it’s more impressive if you don’t. Here are 8 that (as I type this) for which this blog is the #1 hit (links go to the blog address that is the hit):

There was at least one other which I’m having trouble remembering at the moment. Perhaps I’ll update later if I remember what it was.

Microbial Fuel Cell netcast…

It’s only my first attempt at anything like this, so constructive comments are welcome…

(Hopefully you can see the embedded audio player here…)For those of you just tuning in, this is a 90-second explanation of Why Microbial Fuel Cells work. A longer (though still simple) explanation can be found at a slightly older post here.[Update: this was featured in the November 6, 2007 broadcast! Hooray, I can now claim to be an international “radio personality”!]Presuming hosting this file doesn’t kill my bandwidth, I’ll leave it up here. BelowAbove, you should see an embedded flash player (assuming you have Macromedia® Flash® player installed) which you should be able to click on to start the audio. I’ll also place a direct download link below. It should be noted that like everything else on this blog (unless otherwise specified), this audio is also available under the Creative Commons non-commercial/attribution/share-alike license, so as long as you have no problem with the terms of that license you are welcome to copy, redistribute, put up on bittorrent, host a public performance, turn into an interpretative dance art project, or whatever else you might want to do with it so long as you give me credit for it, don’t use it for commercial purposes, and distribute any derivative works of it under the same terms.

You can download the audio directly from here – right-click on the link and select “save link as…”. Ogg Vorbis format available on request…

Poor-boy science: should I build my own electrophoresis platform?

I want to build my own little electrophoresis gizmo to play with.

I did pick up a small tube of powdered graphite and some liquid tape. With this, I should be able to make a waterproof electrically-conducting glue that I can use for the electrodes. I’ve got numerous old “wall-wart”-type power adapters that I ought to be able to use for power supply.

The main thing I’m trying to work out in my head before I start trying to actually put this together is exactly how I’m going to arrange it so that I can have either a thin gel or a piece of paper or other fibrous material in between the electrodes so that I can best separate things.

I suppose it’s kind of bizarre, but this is actually part of the ongoing Expired JellO® projects. I was wondering to myself what actual changes might possibly occur in a packet of dry gelatin mix over time, and how would I be able to tell?  My previous experiments have shown no indication that there are any easily detectable differences (no obvious changes in taste or texture, no strange eerie glow, no acquisition of superpowers upon eating it…) so I’ll have to look more closely.

It occurred to me that just maybe over time the strands of protein that make up gelatin might get damaged by oxidation from the air in the pouch (or do they seal the pouch in a relatively inert gas, like argon or nitrogen?). This isn’t something one can really tell just by looking, obviously. One MIGHT be able to tell indirectly by making fresh and “expired” packets of gelatin with the same precisely-measured amount of water, poured on at the same precisely-measured temperature, and ideally with the same amount of mixing. Believe it or not, there are actually special scientific devices for measuring the firmness of gels like this. The hypothesis would be that expired gelatin might end up “degraded” into smaller strands of protein than a fresh packet, and that this would be reflected in a reduced firmness of the gel, or perhaps reduced water-holding capacity.

However, I don’t have access to precise devices for measuring things like that, and in any case since I suspect the difference would be pretty minimal, I’m not sure any difference in firmness would really be detectable with any kind of instrument I could cobble together on my own. What to do?…

I thought that if I had a way to subject a sample of dissolved gelatin to electrophoresis, I could then use a protein-staining substance to see how broad of a range of protein-fragment sizes were existent, or perhaps even spot distinct fragments if oxidative damage tended to happen at the juncture between particular amino acids or something.

I’m not quite sure why, but I have a strong desire to do this experiment from scratch as a “hillbilly biotech” exercise (including building the equipment and obtaining my supplies from grocery or hardware stores rather than specialty scientific supply places).

There are special protein staining compounds I can use at the end to see where my bits of protein ended up after electrophoresis. “Coomassie Brilliant Blue“, for example, but they don’t have that down at the grocery store. (And if you think that’s a funny name for a dye, consider “Light Green SF Yellowish”…)

Then, I ran into a post indirectly about henna over on scienceblogs.com. It seems the natural orange-staining ingredient in henna, called lawsone, may be specifically a protein-staining substance. I’m not certain about this, but a dark-orange protein-staining dye would work for my purposes I think. If so, that solves my need to get a protein stain from an ordinary store.

It’ll be a little while before I can try to put this plan into action, but I think I’ll be able to get to it in the next month or two.

In other news, I think I’ll try to post my “Microbial fuel cells in 90 seconds” audio sometime tomorrow. Then I can work on more. Anybody want to hear me attempting to explain something in 90 seconds? So far I’ve considered MRSA, and perhaps how cow flatulence threatens the world’s climate (which is also a microbiological topic). I’m sure there must be plenty of other possible topics. Any suggestions?

P.S. Who wants audio in Ogg Vorbis format in addition to mp3?

Electricity-breathing bacteria! (Microbial fuel cells)

I made a 90-second “pod”cast of why microbial fuel cells work. I don’t yet know if This Week in Science is or was interested in playing it. [Update: this was featured in the November 6, 2007 broadcast! Hooray!] Either way, once I find a way to make it available without killing my bandwidth I shall. I’ll probably do more of them – if nothing else I obviously need the practice.

It was oddly difficult getting myself to actually talk to the microphone – more so than actually publically speaking to real people. I’m not sure why. It strikes me as something I’ll get over quickly once I’ve done it a few times, and my voice won’t sound quite so bland in the future.

In any case, microbial fuel cells are possibly the topic that got me really interested in a college education in applied biotechnology. I’ve been meaning to do a post on why they work for a while, so here’s one, in somewhat more detail than the 90-second audio version.

First, some quick review: We all remember that atoms are made of positively-charged protons, uncharged neutrons, and negatively-charged electrons, right? Protons and usually neutrons in the middle, and electrons hovering around. When atoms chemically react with each other, they’re really just having a fight over who gets to keep the electrons. When the reaction is over, some kinds of atoms or groups of atoms will have gained at least partial custody of electrons that used to belong to some of the other atoms or groups of atoms. The ability of a kind of atom to take electrons away from other atoms is called “electronegativity”. The second most electronegative element in the universe just happens to be a major part of our atmosphere – Oxygen.

As bacteria break down food molecules to get biological energy, there are electrons left over along the way. The bacterial cells have specific carrier molecules that take these extra electrons away, where they can be later dumped elsewhere into any of a variety of other useful biological reactions that need them. The one we’re concerned with today is called the Electron Transport Chain.

In many bacteria, and in the mitochondria of plants, fungi, and animals, the Electron Transport Chain regenerates a huge amount of a cell’s biochemical energy. The extra electrons get sucked into the beginning of this chemical chain, and as they are pulled along, the force of this pull drives a process which regenerates the cells’ main energy-carrying molecule, called ATP. This process is “respiration”, and it’s also exactly the reason you need to breathe oxygen. Humans need so much energy just to remain alive that we couldn’t survive without the huge amount of extra energy that respiration provides.

What drives this whole chain is some chemical at the other end pulling the electrons out. In aerobic organisms, this is oxygen. Some bacteria can use other chemicals, like nitrates, sulfates, and ferric iron (yes, there are bacteria that can breathe rust…) None of these chemicals provide quite as much energy as oxygen does, but it’s better than nothing and gives bacteria that could be damaged by oxygen something to breathe.

Normally, this last step happens inside the cell, but some bacteria have ways of extending this last step so that the final hand-off of the electrons happens outside itself. Some bacteria even make electrically-conducting biological “nano-wires” that this can happen through. Others make “shuttle” molecules that can pick up electrons, dissolve out of the cell, hand off the electrons somewhere outside, and then dissolve back into the cell to pick up more.

Now, we can make a microbial fuel cell. An electrode is put where the bacteria are growing – without oxygen – and a wire runs from this, out of the area where the bacteria are and to another electrode which is exposed to oxygen. It’s like an electric snorkel for bacteria. From the electrode and through the wire, the oxygen sucks electrons away from the bacteria. An electrical device stuck between the ends of the wire can use this energy exactly the same way that it could use the energy from electrons being sucked from one end of a battery to another.

Interestingly, the common “simple stain” Methylene Blue can also act as an artificial “shuttle” molecule. When reduced (carrying extra electrons) methylene blue is actually colorless, and I would swear I’ve seen protocols somewhere that use this to measure just how active a yeast culture is, and one of the demonstration microbial fuel cell setups actually uses a culture of yeast in methylene blue rather than a microbe that can naturally breath through electrodes.

By the way, if you thought you could tell a human from a realistic humanoid robot bent on world domination by the fact that only humans eat, I’ve got bad news for you. One interesting application of microbial fuel cells is Gastrobots. Literally, robots with digestive systems, where bacteria breaking down the contents of the “stomach” act as a microbial fuel cell to power the robot.

I hope you find this explanation useful and interesting. If you have (or even if you haven’t) please let me know. I can’t necessarily tell if I’m doing anybody any good without feedback!

Stir-fried random…

Just a few brief random comments for the moment:

  • Am I the only one who is already completely sick and tired of the word “spooky”?
  • I think I’ve figured out what Descartes’ problem is. He’s gone on this meditation where he’s convinced himself that as far as he knows, nothing exists…except for himself. I think what happens next is that he gets horribly lonely, so when he realizes that his thoughts also exist with him, that’s when he developed that unwholesome passion for them and inability to bear leaving them that I’d previously mentioned. “But what kind of thing am I? I’m a thing that thinks. A thinking thing is what I am. But what kind of thing is that? Oh, yeah, I already said, it’s a thinking thing. Did I mention I was a thinking thing that thinks thoughts?….”. Okay, Descartes, we got it the first time…
  • One of my fellow “college science bloggers whose obscurity currently keeps them low in the vote totals” actually has a pretty neat blog. The Biourbanist focusses on features and attributes of urban areas. Well worth adding to your RSS feeds, I think. After you’ve already voted for me, of course…
  • I am currently attempting to put together my first netcast, in which I shall attempt to crunch an explanation of why microbial fuel cells work, in a form hopefully comprehensible to anyone with a good junior-high-school science education (or a mediocre high-school education, which is probably sadly more common), that fits into 90 seconds. Wish me luck.

More to follow…
UPDATE: Got the “pod”/netcast done – a real blog post on the subject of Microbial Fuel Cells to go with it may be found here tomorrow (Tuesday, October 16th) sometime, so long as nothing unexpected happens…

Do Not Taunt Happy Fun Park

Here’s a brief interlude for my new readers. Members of my immediate family have seen this before elsewhere, but what the heck, I may as well share with you all.

Related to my recent posts about this year’s field-trip to Yellowstone National Park, I am reminded of a trip my wife and I took last year to Norris Geyser Basin in the same park.

I’ve heard of “communing with nature”, when the natural world seems to speak to you and put you at ease. Well, on this occasion it didn’t just seem to be speaking to me, and it hardly put me at ease. The conversation between me and the park went something like as follows that day. (Forgive all the scrolling, it WAS a several-hour conversation after all. If it bugs you, feel free to say so in the comments…)

Sign:No Restroom in Geyser Basin

Well, okay, I don’t smoke, I didn’t bring a bicycle, we left the dog at home. And I guess we can hold it until later. It’s a small price to pay to go out to nice, happy, peaceful trails, away from, for example, all the annoying road construction.Traffic cone, in the middle of the trailWow! Look at that! Do I spy the Fruiting Body of the rare Yellowstone Giant Orange Holewarning Mushroom?!?!?No, wait…that’s just a traffic cone over a hole in the trail! What the heck? I thought I was getting away from road construction!

Well. Maybe things will get more natural-looking once we get a chance to walk off into the wilderness. Maybe the map’ll show where we can go.

Map of Norris Geyser Basin, with Warning to Stay On Designated Trails
Ah, look at all the lovely trails. Plenty of space to roam around in.
What? I can’t leave the trails?
sign:Stay On Designated Trails

Can’t I take a mere step or two off? Just a little bit???

Sign:Stay on TrailSign:Stay On WalkYeah, yeah, whatever. What are you going to do if I don’t – have me arrested?

 

Sign:Unlawful to Leave Walkway
What kind of criminal act could possibly be involved with just leaving the silly walkway? Littering? Vandalism?
Sign:It is UNLAWFUL and UNSAFE to: Leave the walkway in thermal areas or throw objects into or deface thermal features

Oh, come on! Look, there’s a beautiful green pool over there, full of no doubt fascinating little animalcules. Can’t I just go over and take a little look?

Sign:Keep Off - Thermal Area
“Thermal Area”? What the heck is that supposed to mean? It’s a little windy and chilly today, maybe I want to be warmed up a little. So, why not? What’s so bad about a “Thermal” area?

Sign:Hazardous Ground - Thin Crust - Boiling Water

What’s that supposed to mean?

 

Sign:Dangerous Ground -with illustration of kid falling into ground and getting broiled-
Children are prone to explode out of the ground unexpectedly?Walkway shown crossing the top of the steaming opening of Green Dragon SpringWhat the heck? Is Green Dragon Spring actually devouring the ground under that walkway?!?! Oh! I get it – you’re saying the park itself can swallow you up and and cook you?
So everything here is flaming hot death, then, right?

Sign:Warning: Trail My Be Icy

Is there no end to the dangers this place threatens innocent visitors with? Can there possibly be anything else this park can do to us?!?!?

 

Solfatara: Very Dangerous Landscape spewing Sulfuric Acid Gas!
“Thin Crust”? “Boiling Water”? Broiled flesh cooked in acid? Ice?
Is this a park, or the kitchen at a Chinese restaurant? Is this how “Hot and Sour Soup” is made?!?!? Is there nothing that can stand in this realm of violent burning chemical death without fear!?!?!?
Fearless Geyser

But what of us poor, fragile fleshy people? We aren’t safe here!That does it! I’m getting out of here! No more of these horrible Killer Thermal Death Areas of Doom for me! I think maybe I’ll just go look at the nice cuddly animals that Yellowstone is also famous for.
Sign: Caution - Wild Animals are Unpredictable and Dangerous!
This whole friggin’ place wants to gore, dismember, maul, cook, devour, and digest me! That does it. No more of this dangerous stuff for me – I think I’ll just go read a nice book for a while…
Bookstore:Closed
NOOOOOOOOOOOOOOOOOOOOOoooo!!!!!!

Libel! Blasphemy! Slander!…

Injustice! Perfidy! HUMBUG!

Periodically, someone puts up a “could you pass a grade-school science class” quiz. The one linked to the image below goes to one that I just broke down and took, purely out of curiousity. Take a look at this outrage!:

JustSayHi - Science Quiz

Oh, sure, it LOOKS good, but what you don’t see is that it only gave me a 96%, implying that I missed one (it was a short quiz)! Sure, the quiz was very much in the modern fashion for “standardized testing” (aka the “No Child Left Awake” project) where the emphasis is on memorizing stuff for a test rather than actual comprehension. So, I thought, maybe I hadn’t correctly memorized which word was correct for one of the word-memorization questions. But, no, according to the “answer sheet”, the one I supposedly got wrong was this one:

(Note: If you’re planning to actually take that quiz, do so now before you read on and I give away one of the answers…)

“How do mammals respire?”

The options were:

  • Aerobically
  • Anaerobically
  • Both aerobically and anaerobically

Come on, I may hardly ever concern myself with perverse eukaryotic systems but…never mind just “mammals”, as far as I know, all eukaryotes (animals, plants, and fungi) only possess aerobic (oxygen-requiring) respiratory systems.

However, the “answer sheet” for the quiz claims that the answer is “Both aerobically and anaerobically”.

So….they’re wrong. I’m pretty sure what what they were intending to ask, given this answer, is “what kind of metabolism do mammals have?”, in which case their answer is correct.

See, “respiration” is only one part of the cellular energy-generating system. Specifically, it’s our friend, the Electron Transport Chain, which (to grossly oversimplify) harnesses the energy of oxygen sucking electrons off the end of the chain various biochemicals to recharge molecules of ATP. That’s not the only way a cell can get ATP, though. What the quiz authors are presumably alluding to is that there are non-oxygen-requiring biochemical pathways that animal cells can take to make energy – such as the one your muscles use when they can’t get enough oxygen, which involves production of lactic acid, which in turn gets blamed for the “burn” sensation you get when you work your muscles hard.

So, the authors of this quiz are bad, bad people, besmirching my reputation and harming my precious self-esteem by giving me less than 100% on that quiz!

On a related subject: breathing causes cancer in Sprague-Dawley™ rats!

No, seriously, it’s true – try raising one group of Sprague-Dawley™ rats with air, and one group with no air, and examing both populations 150 days later. I guarantee you’ll find many more cancerous growths in the “with air” group than in the group that was denied air to breathe…

What brought this outburst on? It was this blog article. “No, It’s for Real: Aspartame Causes Cancer”, the post proclaims. They’re talking about This study(pdf). Go ahead, take a look, but in particular, look at the tables of actual data, not the paper’s abstract. In particular, take a look at Figure 1, especially “D” and “E” (showing survival rates for the different groups of Sprague-Dawley™ rats as the study progressed), and at the number of “tumor-bearing animals” in Table 2.

Notice that at around 120 days on the survival graphs, the groups with the highest percentage of members still alive were the groups receiving the most aspartame in their feed. It’s worth noting that the highest-Aspartame group there was getting roughly the equivalent of a human drinking <em>thousands</em> of cans of diet soda every day. Also note, in fairness, that both graphs seem to show little difference between the groups, so rather than assuming that Aspartame makes Sprague-Dawley™ rats live longer, I would tend to assume that there’s really not much difference.

Notice also that in terms of the percentage of Sprague-Dawley™ rats that developed one or more tumors, there were fewer of them in the group that got the equivalent of 500 mg/kg of aspartame: which scaled up to human terms means about 200-250 cans of diet soda EVERY DAY worth of aspartame.

You may be wondering why I keep mentioning Sprague-Dawley™. It’s because this is a particular commercially-bred strain of rat that’s popular with labs for this kind of thing. One point that isn’t always mentioned is this: Sprague-Dawley™ rats are known to be prone to developing cancer spontaneously. This can be handy if you’re doing studies of “borderline” carcinogens. The hope is that if something has even a tiny ability to cause cancer, you’ll be able to measure the effect in a population of critters known to get cancer at the drop of a metaphorical hat, when in a human population the incidence might be so rare that you can’t distinguish it from random chance. To my admittedly-not-big-on-the-biochemistry-of-perverse-eukaryotes mind, this study really seems to show that there’s little or no effect – and certainly no dose-dependent effect – of aspartame even on cancer-prone lab rats.

I don’t know what it is, but “artificial sweeteners”, and especially aspartame, seem to generate such passionate hatred in some people. It reminds me a great deal of people’s reactions to “genetically modified” crops. People just really want to hate it. The authors of this paper are obviously trying REALLY hard to show somehow that aspartame is a dangerous poison, despite the inconclusive-appearing actual results. Though I suppose one could argue that they showed Aspartame to be at least as much of a deadly poison as Expired JellO®.

And now that I have exposed my readers to several times the Recommended Daily Allowance of Humbug, I bid you all a good night – I have Art History and Philosophy to attend in the morning…

Environmental Chemistry Field Trip – Day 1, part 3

Overview of Narrow Gauge Spring
Our final destination of the day was Narrow Gauge Spring, which is on the backside of the Mammoth Terraces area. Apparently, there’s only one other place in the entire world – somewhere in China – that has exactly the same kind of conditions as this place.

The process of making this kind of formation requires rainwater, healthy microbe-supporting soil, limestone, and heat. It goes something like this: rainwater seeps down through the soil, where lots of healthy microbial activity uses up the oxygen in it and excretes plenty of extra carbon dioxide into it, making it more acidic. The water sinks into the ground and runs into the limestone, which is Calcium Carbonate (CaCO3). Calcium Carbonate doesn’t dissolve well in plain water at all, but there are two things that make it dissolve better: acid and heat. The heat from the magma under the park and the acidity of the water combine to dissolve a whole lot of the limestone. Then, somewhere, the heated water gets forced back up to the surface through a crack.

Where the water comes back in contact with the air, it can let off the extra carbon dioxide and heat. This doesn’t happen very fast in a deep pool, since this can only happen in a thin area near the top. Where the water overflows, though, it’s very shallow, and the carbon dioxide and heat can escape very quickly into the air. This makes the water suddenly become less acidic and less hot, and all that extra calcium carbonate can no longer stay dissolved. It crystallizes, making a hard calcium carbonate “shell” along the edge of the pool. The edge can end up growing some much over time that it forms an overhang with stalactite-like formations underneath it:

Another view of Narrow Gauge Spring

You can just make out an overhanging area in the upper-left of the photograph.

It was fun taking measurements of the water here. Water freshly removed from a pool initially showed up off the scale on our “Total Dissolved Solids” meters, but if you waited a few seconds the reading would drop down to where the meters could read it, and keep falling. Out of the pool, the water was cooling off quickly enough that the extra dissolved Calcium Carbonate was un-dissolving out of the water in tiny bits even as we stood there.

The water appeared to be about 56°C at the top of the pool where it was initially emerging. If you want an idea of not only that I am a nerd but what kind of nerd I am, I will mention that I think of this as “stewpot temperature”, and often wonder if there is any useful or tasty effects to be discovered in the microbial processes done by thermophilic microbes that live in these conditions. I’ll find out one of these days…

Oh, and a couple of bits of trivia about the Apollinaris Spring area from a couple of posts ago. Firstly, it was apparently named after a spring in Germany with the same name. Secondly, we briefly discussed the chemistry of carbon dioxide in water in class this week, and it turns out that the pH of 5.9 that Apollinaris Spring has is probably more basic than plain distilled water would be.

Now, anyone who’s had basic chemistry is probably a little baffled by this – after all, isn’t a pH of 7 that of pure water by definition? The answer is yes, but we’re not talking about pure water, we’re talking about water exposed to the air, where carbon dioxide can dissolve into the water. Working through the mathematics involved showed that distilled water should end up with a pH of about 5.6-5.7, at least at “standard temperature and pressure” (roughly sea-level air pressure and a temperature of around 72°F.). I have a suspicion as to why the Apollinaris Spring water seems less acidic than I might have expected, though.

They actually took our Apollinaris Spring water and ran it through an analytical instrument of some kind (I wasn’t there for it, but the description of the results made it sound like it was a “liquid chromatography” type of device). They found NO nitrates or nitrites in it. Since we’re talking about spring water percolating through healthy soil, I would have expected some nitrogen. I noticed, though, that although they checked for nitrite and nitrate, they didn’t check for reduced nitrogen – that is, ammonia.

I managed to score a tiny vial of the water during lab last Wednesday. When I get a chance to hit the pet store for some ammonia testing supplies, I’ll check that. If it’s there, it might explain the possibly slightly higher than expected pH. Similar to what happens to carbon dioxide and water, when ammonia (NH3) is dissolved into water(H2O), there tends to be some recombination of the atoms to make “ammonium hydroxide” (NH4OH), which is basic.

I don’t know if that’s what’s going on, but I intend to check.

There’s one more post worth of Field Trip stuff, and then I’ll be back onto other topics. Here’s a hint of what might come up, though: can anybody tell me what the effective pore size of pectin and cornstarch gels might be?…